Question: How Can I Convert Impute2 (.Haps .Sample) To Plink (.Map .Ped)?
gravatar for Kyle Oliveira
7.2 years ago by
Kyle Oliveira50 wrote:

I have phased data output from SHAPEIT in .haps and .sample formats. I need to convert it back to PLINK formats (probably .map and .ped) so I can perform some further analyses.

Does anyone know how I could do that? I'm not having a lot of luck looking at the pages for PLINK, IMPUTE2, and SHAPEIT...

plink • 7.6k views
ADD COMMENTlink written 7.2 years ago by Kyle Oliveira50
gravatar for Caddymob
7.2 years ago by
United States
Caddymob950 wrote:

Use GTOOL for PED to GEN Conversion,

I tend to do it like this, the log file can be quite large and is generally useless so I send it to nowhere.

gtool -G --g CHR${i}.IMPUTE2.phase --s YourStudy_Chr${i}.IMPUTE2.sample --ped CHR${i}.ped --map CHR${i}.map --phenotype Phenotype --sex Gender --log /dev/null
ADD COMMENTlink written 7.2 years ago by Caddymob950

I'm exploring that route now, but it looks about right. Thanks!

ADD REPLYlink written 7.2 years ago by Kyle Oliveira50


sure about that ? The format out of shapeit is not a genotype but haplotyped. Is the -G working OK ?

ADD REPLYlink written 7.2 years ago by Genotepes940


I am facing the same problem currently, I have shapeit phased haplotypes and want to calculate LD using plink. So I need to convert my .hap file to .gen (can be directly used by plink1.9) or .ped format (plink 1.7). Referring to the last comment of Genotepes: No, at least for me the "-G" doesn´t work. Would be super if somebody would read this (pretty old^^) thread :-) And it would be supersuper if somebody could help me - my question is, how do I convert the .hap to a .gen/.ped format??

BW Linda

ADD REPLYlink written 4.6 years ago by van-den-Berg20
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